The csv file “Samples Report of 20180710-Lisa-fullsetDIA.csv” was used. The original data has 224 variables. The variable “DECOY_sp|P04114|APOB_HUMAN” was removed.
The mean of count for responders and non-responders before and after treatment.
The mean of intensity for responders and non-responders before and after treatment.
Below is a barplot of number of proteins with missing values. There are 9 variables with 1 missing values, 5 with 2 missing values, and there are 81 proteins that none of the samples has a value.
Proteins with morer than 5 missing values were removed. For the rest proteins, missing values were filled up using 1/2 of the lowest value.
Below is the barplot of the sum of each sample’s count. This shows that the total amount of peptides are relatively equivalent between samples.
## Coefficients not estimable: Subject123
Responding + Timepoint + Responding * Timepoint + Subject + 1
The Responding * Timepoint coefficient was tested.
Below is the distribution of the p values
Vocano plot. Only one protein, Anthrex toxin receptor 1, has a p value < 0.05. Not a typical HDL protein.
Below is the statistic result for each protein.
Boxplot of Anthrax toxin receptor 1